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- EMDB-64672: GPR133-Gain-miniG13 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-64672
TitleGPR133-Gain-miniG13 complex
Map data
Sample
  • Complex: GPR133-Gain-miniG13-Gbeta1-Ggamma2 complex
    • Protein or peptide: Adhesion G-protein coupled receptor D1
    • Protein or peptide: Guanine nucleotide-binding protein subunit alpha-13,Isoform 2 of Guanine nucleotide-binding protein subunit alpha-13
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
KeywordsGPCR / G12/G13 / Complex / Stachel / MEMBRANE PROTEIN
Function / homology
Function and homology information


D5 dopamine receptor binding / regulation of skeletal muscle contraction / regulation of fibroblast migration / Rho-activating G protein-coupled receptor signaling pathway / regulation of small GTPase mediated signal transduction / NRAGE signals death through JNK / branching involved in blood vessel morphogenesis / CDC42 GTPase cycle / regulation of postsynapse assembly / Rho protein signal transduction ...D5 dopamine receptor binding / regulation of skeletal muscle contraction / regulation of fibroblast migration / Rho-activating G protein-coupled receptor signaling pathway / regulation of small GTPase mediated signal transduction / NRAGE signals death through JNK / branching involved in blood vessel morphogenesis / CDC42 GTPase cycle / regulation of postsynapse assembly / Rho protein signal transduction / RAC1 GTPase cycle / guanyl-nucleotide exchange factor activity / brush border membrane / G protein-coupled receptor activity / platelet activation / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / regulation of blood pressure / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / G-protein activation / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through CDC42 / Glucagon signaling in metabolic regulation / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / ADP signalling through P2Y purinoceptor 12 / Sensory perception of sweet, bitter, and umami (glutamate) taste / photoreceptor disc membrane / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / cellular response to catecholamine stimulus / ADP signalling through P2Y purinoceptor 1 / ADORA2B mediated anti-inflammatory cytokines production / G beta:gamma signalling through PI3Kgamma / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / adenylate cyclase-activating dopamine receptor signaling pathway / melanosome / GPER1 signaling / Inactivation, recovery and regulation of the phototransduction cascade / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / G alpha (12/13) signalling events / sensory perception of taste / extracellular vesicle / regulation of cell shape / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / retina development in camera-type eye / G protein activity / GTPase binding / Ca2+ pathway / fibroblast proliferation / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / G alpha (i) signalling events / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (q) signalling events / in utero embryonic development / Ras protein signal transduction / cell differentiation / Extra-nuclear estrogen signaling / cell surface receptor signaling pathway / cell population proliferation / postsynapse / nuclear speck / G protein-coupled receptor signaling pathway / lysosomal membrane / focal adhesion / GTPase activity / synapse / protein-containing complex binding / GTP binding / signal transduction / extracellular exosome / nucleoplasm / metal ion binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
G-protein alpha subunit, group 12/13 / Concanavalin A-like lectin/glucanases superfamily / Pentraxin-related / Pentraxin (PTX) domain profile. / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / : / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain ...G-protein alpha subunit, group 12/13 / Concanavalin A-like lectin/glucanases superfamily / Pentraxin-related / Pentraxin (PTX) domain profile. / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / : / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / Concanavalin A-like lectin/glucanase domain superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein subunit alpha-13 / Adhesion G-protein coupled receptor D1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.51 Å
AuthorsXi Y / Pu X / Ping Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32222038 China
CitationJournal: Biochem Biophys Res Commun / Year: 2025
Title: Cryo-EM structural elucidation and molecular mechanism of the GPR133-G13 signaling complex.
Authors: Xuanyu Pu / Yue-Tong Xi / Meng-Xin Wang / Daolai Zhang / Yu-Qi Ping / Peng Xiao / Jin-Peng Sun /
Abstract: GPR133 is an adhesion-class G protein-coupled receptor (GPCR) that has recently been de-orphanized. Its functions are complex and multifaceted. While GPR133 is primarily recognized for coupling with ...GPR133 is an adhesion-class G protein-coupled receptor (GPCR) that has recently been de-orphanized. Its functions are complex and multifaceted. While GPR133 is primarily recognized for coupling with the Gs subunit to mediate elevated intracellular cAMP levels, its potential engagement with alternative signaling pathways remains poorly characterized. In our experiments, we demonstrated that GPR133 exhibits constitutive self-activation via its Stachel sequence as an adhesion GPCR, enabling activation of downstream G13 signaling. We reconstituted the GPR133-GAIN-miniGα13 complex in vitro and resolved its cryo-electron microscopy structure at a resolution of 3.51 Å. Detailed structural comparisons between the GPR133-GAIN-miniGα13 complex and the previously resolved GPR133-CTF-Gs structure highlighted both conserved and different features. These findings provide critical insights into the signal transduction mechanisms of GPR133 and lay a foundation for targeted therapeutic strategies.
History
DepositionMay 19, 2025-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64672.png

Downloads & links

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Map

FileDownload / File: emd_64672.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 250 pix.
= 232.5 Å		0.93 Å/pix.
x 250 pix.
= 232.5 Å		0.93 Å/pix.
x 250 pix.
= 232.5 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.001788004 - 2.1502366
Average (Standard dev.)0.0012796992 (±0.02629943)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 232.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64672_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_64672_half_map_2.map
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Sample components

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Entire : GPR133-Gain-miniG13-Gbeta1-Ggamma2 complex

EntireName: GPR133-Gain-miniG13-Gbeta1-Ggamma2 complex
Components
  • Complex: GPR133-Gain-miniG13-Gbeta1-Ggamma2 complex
    • Protein or peptide: Adhesion G-protein coupled receptor D1
    • Protein or peptide: Guanine nucleotide-binding protein subunit alpha-13,Isoform 2 of Guanine nucleotide-binding protein subunit alpha-13
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

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Supramolecule #1: GPR133-Gain-miniG13-Gbeta1-Ggamma2 complex

SupramoleculeName: GPR133-Gain-miniG13-Gbeta1-Ggamma2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Adhesion G-protein coupled receptor D1

MacromoleculeName: Adhesion G-protein coupled receptor D1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 65.688828 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: HPIITNLTEE RKTFQSPGVI LSYLQNVSLS LPSKSLSEQT ALNLTKTFLK AVGEILLLPG WIALSEDSAV VLSLIDTIDT VMGHVSSNL HGSTPQVTVE GSSAMAEFSV AKILPKTVNS SHYRFPAHGQ SFIQIPHEAF HRHAWSTVVG LLYHSMHYYL N NIWPAHTK ...String:
HPIITNLTEE RKTFQSPGVI LSYLQNVSLS LPSKSLSEQT ALNLTKTFLK AVGEILLLPG WIALSEDSAV VLSLIDTIDT VMGHVSSNL HGSTPQVTVE GSSAMAEFSV AKILPKTVNS SHYRFPAHGQ SFIQIPHEAF HRHAWSTVVG LLYHSMHYYL N NIWPAHTK IAEAMHHQDC LLFATSHLIS LEVSPPPTLS QNLSGSPLIT VHLKHRLTRK QHSEATNSSN RVFVYCAFLD FS SGEGVWS NHGCALTRGN LTYSVCRCTH LTNFAILMQV VPLELARGHQ VALSSISYVG CSLSVLCLVA TLVTFAVLSS VST IRNQRY HIHANLSFAV LVAQVLLLIS FRLEPGTTPC QVMAVLLHYF FLSAFAWMLV EGLHLYSMVI KVFGSEDSKH RYYY GMGWG FPLLICIISL SFAMDSYGTS NNCWLSLASG AIWAFVAPAL FVIVVNIGIL IAVTRVISQI SADNYKIHGD PSAFK LTAK AVAVLLPILG TSWVFGVLAV NGCAVVFQYM FATLNSLQGL FIFLFHCLLN SEVRAAFKHK TKVWSLTSSS ARTSNA KPF HSDLMNGTRP GMASTKLSPW DKSSHSAHRV DLSAV

UniProtKB: Adhesion G-protein coupled receptor D1

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Macromolecule #2: Guanine nucleotide-binding protein subunit alpha-13,Isoform 2 of ...

MacromoleculeName: Guanine nucleotide-binding protein subunit alpha-13,Isoform 2 of Guanine nucleotide-binding protein subunit alpha-13
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.705596 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MMGSTVSAED KAAAERSKEI DKCLSREKTY VKRLVKILLL GADNSGKSTF LKQMRIIHGG SGGSGGTKGI HEYDFEIKNV PFKMVDVGG QRSERKRWFE CFDSVTSILF LVDSSDFNRL TESLNDFETI VNNRVFSNVS IILFLNKTDL LEEKVQIVSI K DYFLEFEG ...String:
MMGSTVSAED KAAAERSKEI DKCLSREKTY VKRLVKILLL GADNSGKSTF LKQMRIIHGG SGGSGGTKGI HEYDFEIKNV PFKMVDVGG QRSERKRWFE CFDSVTSILF LVDSSDFNRL TESLNDFETI VNNRVFSNVS IILFLNKTDL LEEKVQIVSI K DYFLEFEG DPHCLRDVQK FLVECFRNKR RDQQQKPLYH HFTTAINTEN ARLIFRDVKD TILHDNLKQL MLQ

UniProtKB: Guanine nucleotide-binding protein subunit alpha-13, Guanine nucleotide-binding protein subunit alpha-13, Guanine nucleotide-binding protein subunit alpha-13

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Macromolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.861143 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

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Macromolecule #4: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.784301 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GSLLQSELDQ LRQEAEQLKN QIRDARKACA DATLSQITNN IDPVGRIQMR TRRTLRGHLA KIYAMHWGTD SRLLVSASQD GKLIIWDSY TTNKVHAIPL RSSWVMTCAY APSGNYVACG GLDNICSIYN LKTREGNVRV SRELAGHTGY LSCCRFLDDN Q IVTSSGDT ...String:
GSLLQSELDQ LRQEAEQLKN QIRDARKACA DATLSQITNN IDPVGRIQMR TRRTLRGHLA KIYAMHWGTD SRLLVSASQD GKLIIWDSY TTNKVHAIPL RSSWVMTCAY APSGNYVACG GLDNICSIYN LKTREGNVRV SRELAGHTGY LSCCRFLDDN Q IVTSSGDT TCALWDIETG QQTTTFTGHT GDVMSLSLAP DTRLFVSGAC DASAKLWDVR EGMCRQTFTG HESDINAICF FP NGNAFAT GSDDATCRLF DLRADQELMT YSHDNIICGI TSVSFSKSGR LLLAGYDDFN CNVWDALKAD RAGVLAGHDN RVS CLGVTD DGMAVATGSW DSFLKIWN

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7ept

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.51 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 45759
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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